Contacts of the strand formed by residues 333 - 337 (chain A) in PDB entry 1JPK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 4.0 7.4 + - - +
31A THR* 3.6 41.6 + - + +
32A PRO* 3.9 8.1 - - - +
292A ARG* 4.0 3.1 - - - +
300A THR* 3.8 2.0 - - - +
301A LEU 3.2 12.1 - - - -
303A GLY* 3.3 40.2 + - - -
324A MET* 3.5 17.2 - - - +
325A LEU* 4.0 20.8 - - + +
328A PHE* 3.4 47.0 - + + -
329A GLY 3.9 12.8 - - - +
330A PRO 4.8 3.2 + - - +
331A HIS 3.3 9.8 - - - +
332A ARG* 1.3 78.3 - - - +
334A ILE* 1.3 74.8 + - - +
335A ALA* 3.7 9.8 - - + +
365A ARG* 5.8 0.9 + - - -
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.0 26.0 - - + +
22A ALA* 3.9 14.6 - - + -
23A ALA* 4.0 20.2 - - + +
32A PRO* 3.8 14.6 - - + +
34A TRP* 4.0 12.8 - - + -
279A VAL* 4.1 11.9 - - + -
300A THR* 3.9 19.1 - - + -
301A LEU 3.0 8.6 + - - +
302A GLN* 3.1 24.5 - - + +
303A GLY 2.6 32.6 + - - -
333A TYR* 1.3 79.1 - - - +
335A ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 3.7 8.0 - - + +
32A PRO 2.9 9.6 + - - +
33A VAL* 3.4 23.1 - - + -
34A TRP* 3.5 3.6 + - - -
324A MET* 4.9 1.6 - - + -
325A LEU* 4.9 0.4 - - + -
333A TYR* 3.7 20.9 - - + +
334A ILE* 1.3 76.2 - - - +
336A ASN* 1.3 66.6 + - - +
353A PHE* 4.8 1.3 - - + -
357A VAL* 3.5 40.8 - - + -
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 2.8 63.9 + - - +
35A CYS* 3.3 1.0 - - - -
36A MET* 3.2 26.3 + - + +
302A GLN* 3.9 21.6 - - + +
303A GLY 2.5 29.9 + - - +
305A LEU* 3.2 4.9 + - - +
334A ILE 3.8 0.2 + - - -
335A ALA* 1.3 76.5 - - - +
337A LEU* 1.3 85.3 + - - +
353A PHE* 3.6 17.3 - - - -
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A CYS* 4.2 11.4 - - + -
36A MET* 3.3 16.9 - - - +
282A LEU 4.2 2.6 - - - +
302A GLN 5.5 0.3 - - - +
304A ASN* 3.7 5.5 + - - -
305A LEU* 3.3 28.3 - - + +
307A PRO* 4.3 13.2 - - + -
310A LEU* 4.1 17.0 - - + -
336A ASN* 1.3 93.0 + - - +
338A GLY* 1.3 59.2 + - - +
339A HIS 3.2 23.1 - - - +
341A LEU* 3.5 39.7 - - + +
353A PHE* 4.0 26.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il